Spring Creek downstream from Iron Mountain Mine contains some of the most acidic water ever measured.Image courtesy Gene Tyson/UC Berkeley.

Iron Mountain Mine in Northern California was once the largest source of toxic metals in the United States. A century of mining for gold and other metals unearthed rocks that, when exposed to the air, released acid and heavy metals into the water underground.

Miners who accidentally left their shovels at the site overnight were likely to return the next day to find half a shovel eaten away by the corrosive water. Surrounding creeks were stained red from the pollution. Cleanup began in 2000 to control runoff from the mine into the Sacramento River.

Genome Sequences Yield Insights

To understand this toxic wasteland, scientists have sequenced the genomes of a small community of hearty microbes that lives in Iron Mountain. The microbes actually accelerate toxic runoff from the mine so studying their genomes could help researchers understand how to clean up the environment.

But the microbes don’t survive outside the mine. So instead of isolating individual microbes to study, the researchers extract and analyze DNA from all the organisms in a sample of water.

By analyzing the pooled DNA from all the microbes, it then becomes possible to assemble the genomes of individual species and identify their genes. From there, the next step is to correlate what is known about those genes with what the microbes actually do.

Iron Mountain is one of the first examples of scientists sequencing the whole genomes of organisms from a community of microbes in nature—a new area of biology called community, or environmental, genomics. Jill Banfield of the University of California at Berkeley led the research.

“What was interesting about Iron Mountain is that before we started, we didn’t have much idea what was there,” says Jim Bristow of the Joint Genome Institute in Walnut Creek, California, which did the sequencing.

Throughout the world, researchers are using environmental genomics as a first step in describing the vast, unseen realm of microbes in the soil and the oceans to better understand how they affect the environment and energy cycles.

Banfield has nicknamed the microbes “champion extremophiles” because of the extreme conditions in which they thrive.

The microbes live hundreds of feet underground where there is no sunlight and nutrients are scarce. They live in water that is 120 degrees Fahrenheit (50 degrees Celsius) and is chock full of arsenic, zinc and copper—as caustic as battery acid.

The eccentric organisms encase themselves in a pink “biofilm” that floats on the water flowing in the mine, keeping the microbes in contact with both the air and water to collect nutrients.

To collect samples, the researchers travel through a mile of tunnels to the center of the mine. They wear hard hats, protective glasses, white plastic suits, and blue gloves. Thick rubber boots protect their feet from the acidic water.

They sequenced the genomes of five previously unknown organisms that live in Iron Mountain. The corrosive microbes are a mixture of bacteria and Archaea, an ancient domain of life that is separate from animals, plants, and bacteria. They found two types of bacteria called Leptospirillum, another called the G-plasma microbe, and three types of Archaea called Ferroplasma.

Now, Banfield is using the genome sequences to build DNA microarrays that she can use to study what the microbes do because the process they use to make energy actually accelerates toxic runoff from the mine.

Yellow fluorescent dots show Leptospirillum bacteria in a sample taken from Iron Mountain. Blue dots show Archaea.Image courtesy Nature.

Environmental Genomics

Iron Mountain is not the only place from which biologists hope to uncover communities of microbes. Environmental genomics is helping researchers study all kinds of organisms that are difficult to grow outside their environment.

In separate projects, scientists at The Institute for Genomic Research in Rockville, Maryland, are sequencing microbes that live inside human intestines. Researchers at the Institute for Biological and Energy Alternatives, also in Rockville, are collecting, sequencing, and describing microbes from the Sargasso Sea near Bermuda.

Meanwhile, the Joint Genome Institute has launched a new project, called the Community Sequencing Program, to sequence more communities of organisms like those at Iron Mountain.

The complexity of some environments will be a challenge to researchers as they try to pull out complete genomes from diverse environments with many species. Banfield admits that her project was a lot easier than it could have been because it was a small community of microbes.

Banfield says she considers herself a geologist first. Her foray into genomics and “champion extremophiles” is just the most logical way to figure out more about the geological and chemical processes underway at Iron Mountain.

Tyson, G.W. et al. Insights into community structure and metabolism by reconstruction of microbial genomes from the environment. Nature (Published online February 1, 2004).